Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation

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2021-07-01Author
Van Poucke, Kris
Haegeman, Annelies
Goedefroit, Thomas
Focquet, Fran
Leus, Leen
Horta Jung, Marília
Nave, Corina
Redondo, Miguel Ángel
Husson, Claude
Kostov, Kaloyan
Lyubenova, Aneta
Christova, Petya
Chandelier, Anne
Slavov, Slavtcho
De Cock, Arthur
Bonants, Peter
Werres, Sabine
Marçais, Benoit
Jung, Thomas
Stenli, Jan
Ruttink, Tom
Heungens, Kurt
Suggested citation
Van Poucke, Kris;
Haegeman, Annelies;
Goedefroit, Thomas;
Focquet, Fran;
Leus, Leen;
Horta Jung, Marília;
...
Heungens, Kurt.
(2021)
.
Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation.
IMA Fungus, 2021, vol. 12, art. 16 (1-24).
https://doi.org/10.1186/s43008-021-00068-w.
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The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species
have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a
wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose
a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is
therefore essential for adequate plant protection but this is hampered by the limitations of morphological and
traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning
of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we
have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614
Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-
specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid
species and discover 16 new hybrid species. Our method was also valuable for species identification at an
unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a
concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS
data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in
this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow
cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations
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IMA Fungus, 2021, vol. 12, art. 16 (1-24)European research projects
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